[2023-03-15 13:52:04,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:52:04,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:52:04,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference
[2023-03-15 13:52:05,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:52:05,806] [INFO] Task started: Prodigal
[2023-03-15 13:52:05,806] [INFO] Running command: cat /var/lib/cwl/stg822bc412-a957-4a7a-9624-3cad4a691cd9/OceanDNA-b2417.fa | prodigal -d OceanDNA-b2417/cds.fna -a OceanDNA-b2417/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:52:10,325] [INFO] Task succeeded: Prodigal
[2023-03-15 13:52:10,326] [INFO] Task started: HMMsearch
[2023-03-15 13:52:10,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b2417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/reference_markers.hmm OceanDNA-b2417/protein.faa > /dev/null
[2023-03-15 13:52:10,521] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:52:10,522] [INFO] Found 6/6 markers.
[2023-03-15 13:52:10,533] [INFO] Query marker FASTA was written to OceanDNA-b2417/markers.fasta
[2023-03-15 13:52:10,534] [INFO] Task started: Blastn
[2023-03-15 13:52:10,534] [INFO] Running command: blastn -query OceanDNA-b2417/markers.fasta -db /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/reference_markers.fasta -out OceanDNA-b2417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:52:11,080] [INFO] Task succeeded: Blastn
[2023-03-15 13:52:11,082] [INFO] Selected 11 target genomes.
[2023-03-15 13:52:11,082] [INFO] Target genome list was writen to OceanDNA-b2417/target_genomes.txt
[2023-03-15 13:52:11,090] [INFO] Task started: fastANI
[2023-03-15 13:52:11,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg822bc412-a957-4a7a-9624-3cad4a691cd9/OceanDNA-b2417.fa --refList OceanDNA-b2417/target_genomes.txt --output OceanDNA-b2417/fastani_result.tsv --threads 1
[2023-03-15 13:52:16,374] [INFO] Task succeeded: fastANI
[2023-03-15 13:52:16,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:52:16,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:52:16,375] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:52:16,375] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:52:16,375] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 13:52:16,375] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2417/tc_result.tsv
[2023-03-15 13:52:16,375] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:52:16,375] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:52:16,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/checkm_data
[2023-03-15 13:52:16,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:52:16,381] [INFO] Task started: CheckM
[2023-03-15 13:52:16,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2417/checkm_input OceanDNA-b2417/checkm_result
[2023-03-15 13:52:34,805] [INFO] Task succeeded: CheckM
[2023-03-15 13:52:34,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:52:34,808] [INFO] ===== Completeness check finished =====
[2023-03-15 13:52:34,809] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:52:34,809] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2417/markers.fasta)
[2023-03-15 13:52:34,810] [INFO] Task started: Blastn
[2023-03-15 13:52:34,811] [INFO] Running command: blastn -query OceanDNA-b2417/markers.fasta -db /var/lib/cwl/stg270721b3-a1b5-4c43-a63e-98f1e72b9233/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:52:35,703] [INFO] Task succeeded: Blastn
[2023-03-15 13:52:35,704] [INFO] Selected 10 target genomes.
[2023-03-15 13:52:35,704] [INFO] Target genome list was writen to OceanDNA-b2417/target_genomes_gtdb.txt
[2023-03-15 13:52:35,715] [INFO] Task started: fastANI
[2023-03-15 13:52:35,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg822bc412-a957-4a7a-9624-3cad4a691cd9/OceanDNA-b2417.fa --refList OceanDNA-b2417/target_genomes_gtdb.txt --output OceanDNA-b2417/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:52:37,686] [INFO] Task succeeded: fastANI
[2023-03-15 13:52:37,692] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:52:37,692] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002724835.1	s__Actinomarina sp002724835	98.8312	229	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.97	95.84	0.72	0.71	4	conclusive
GCA_003282445.1	s__Actinomarina sp003282445	92.8633	250	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
GCA_004214055.1	s__Actinomarina sp004214055	84.8983	161	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510995.1	s__Actinomarina sp902510995	83.4751	185	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.36	95.36	0.76	0.76	2	-
GCA_902565645.1	s__Actinomarina sp902565645	81.5625	154	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519845.1	s__Actinomarina sp902519845	77.5782	82	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.50	95.50	0.91	0.91	2	-
GCA_902604835.1	s__Actinomarina sp902604835	77.3381	70	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.34	95.34	0.81	0.81	2	-
GCA_902571385.1	s__Actinomarina sp902571385	77.1442	83	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.95	95.63	0.85	0.83	4	-
GCA_902609285.1	s__Actinomarina sp902609285	76.7448	64	267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:52:37,693] [INFO] GTDB search result was written to OceanDNA-b2417/result_gtdb.tsv
[2023-03-15 13:52:37,693] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:52:37,694] [INFO] DFAST_QC result json was written to OceanDNA-b2417/dqc_result.json
[2023-03-15 13:52:37,694] [INFO] DFAST_QC completed!
[2023-03-15 13:52:37,694] [INFO] Total running time: 0h0m33s